I was able to self-resolve this by stopping the service, dumping the log database file into a SQL File using sqlite3 "Recover" function, then making a new database from that recovered SQL.
From there, I was able to move the new database into the adaxes directory, and name it to AdaxesLog.db3 and Start Adaxes Service Again. All my logs were there including during the time it was malformed.
Of course, ALWAYS backup your log file before running commands on it.
Hope this helps someone in the future with silimar issue:
